It seems ECWolf couldn't find the .WL6 or .SOD-files, due to the fact that I had changed the name of the folder the games were located in from "GOG Games" to "My Games".

Changing back to the original name of the folder fixed it.

EDIT: By the way, is it possible to have ECWolf locate the files in a folder under a different name, and would it also be possible to have mods in a seperate folder that could be loaded through .BAT-files?

For GOG ECWolf should use whatever path you installed it to via the installer. The installer inserted a key in the registry which ECWolf looks up.

Otherwise you can edit the cfg file in %AppData%\ecwolf to point wherever you want, put them in the same directory as the executable, I think it the working directory is also searched by default, or put them in %AppData%\ecwolf. There are also switches to change the directory ECWolf uses for the cfg etc which can be discovered with --help.